● Led investigation of computational rules for CRISPR interference (CRISPRi) guide RNA design optimization, using Python machine learning modules.

● Improved whole-genome targeting of promoter regions in a genome-wide CRISPRi dual-guide library in K562 cancer cell lines.

● Identified over 100 putative therapeutic targets, as computational lead on a CRISPRi screen focused on cellular dysfunction in Niemann-Pick Type C Disease.

● Integrated single-cell epigenetic and transcriptomic data to computationally reconstruct gene regulatory networks for seventy-six transcription factors in iPSC-derived cells.

● Mentored two junior programmers on the computational biology team.

● Co-authored a manuscript officially intended for publication, on in-house experimental findings.

● Quantifed and characterized CRISPR gene modifications in a sickle-cell disease model, with both in-house and open-source tools for genomic data analysis.

● Queried, retrieved, and integrated data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.

● Examined concordance and sensitivity of five computational CRISPR off-target error detection methods.

● Streamlined high-performance analyses for bench scientists via custom data pipelines and user interfaces, enabling round-the-clock analyses.

● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.

● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.

● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.

● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python ML and R to integrate gene panel and RNA-Seq data.

● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.

● Organized and managed close coordination of Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.

● Provided AI and genomic analytic insights in collaboration with Roche-wide data curators and integrators network, to establish F.A.I.R. data management strategies for legacy, current, and next-generation datasets

● Tested data querying capabilities of newly-acquired AWS-based tech stack.

● Scoped design of in-house proteomics assay data ingestion and storage

● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with R statistical and data visualization packages and MATLAB.

● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.

● Spearheaded development of three relational databases derived from Hail population genomics platform, in collaboration with software engineer.

● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.

● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.

● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).

● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.

Topics: Introduction to RNA-Seq, Standard Workflows with DESeq2, Reference-Based Assembly, Exploratory Data Analysis, Statistical Analysis, Data Visualization, Gene Set Enrichment, Variant Annotation

● Presented publication-quality RNA-Seq data summaries and representations to post-doctoral associates

● Presented now-published preprint in contrast with established research at internal Journal Club to inform future experimental design in epigenetic editing.

General Biology II facilitator for two concurrent PLTL courses